Loading report..

Highlight Samples

Regex mode off

    Rename Samples

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      Regex mode off

        Explain with AI

        Configure AI settings to get explanations of plots and data in this report.

        Keys entered here will be stored in your browser's local storage. See the docs.

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.

        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
        Settings are automatically saved. You can also save named configurations below.

        Save Settings

        You can save the toolbox settings for this report to the browser or as a file.

        Load Settings

        Choose a saved report profile from the browser or load from a file:

          Load from File

        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.27

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/metatdenovo analysis pipeline. For information about how to interpret these results, please see the documentation.
        Report generated on 2025-02-05, 16:11 CET based on data in: /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/metatdenovo/.nf-test/tests/374086547a3e73d4a68387d29dc56b00/work/48/be02867500f7502440e663a4ae6c94

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        BBMAP_ALIGNbbmap39.01
        pigz2.6
        samtools1.16.1
        BBMAP_INDEXbbmap39.1
        CAT_FASTQcat9.5
        COLLECT_FEATURECOUNTSR4.2.3
        data.table1.14.8
        dplyr1.1.2
        dtplyr1.3.1
        COLLECT_STATSR4.2.3
        dplyr1.1.2
        purrr1.0.1
        readr2.1.4
        stringr1.5.0
        tidyr1.3.0
        FASTQCfastqc0.12.1
        FEATURECOUNTS_CDSsubread2.0.6
        FORMAT_PRODIGAL_GFFgzip1.11
        HMMER_HMMSEARCHhmmer3.4
        HMMRANKR4.2.3
        tidyverse2.0.0
        MEGAHIT_INTERLEAVEDmegahit_interleaved1.2.9
        PRODIGAL_MODULEpigz2.6
        prodigal2.6.3
        SAMTOOLS_FLAGSTATsamtools1.21
        SAMTOOLS_IDXSTATSsamtools1.21
        SAMTOOLS_INDEXsamtools1.21
        SAMTOOLS_SORTsamtools1.21
        SAMTOOLS_STATSsamtools1.21
        SEQTK_MERGEPEseqtk1.4-r122
        TRANSRATEtransrate1.0.3
        TRIMGALOREcutadapt4.9
        pigz2.8
        trimgalore0.6.10
        UNPIGZ_CONTIGSpigz2.3.4
        UNPIGZ_GFFpigz2.3.4
        WorkflowNextflow24.10.4
        nf-core/metatdenovov1.1dev

        nf-core/metatdenovo Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/metatdenovo

        Methods

        Data was processed using nf-core/metatdenovo v1.1dev of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v24.10.4 (Di Tommaso et al., 2017) with the following command:

        nextflow -quiet -log /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/metatdenovo/.nf-test/tests/374086547a3e73d4a68387d29dc56b00/meta/nextflow.log run /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/metatdenovo/tests/../main.nf -c /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/metatdenovo/nextflow.config -c /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/metatdenovo/tests/nextflow.config -params-file /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/metatdenovo/.nf-test/tests/374086547a3e73d4a68387d29dc56b00/meta/params.json -ansi-log false -profile test,singularity -with-trace /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/metatdenovo/.nf-test/tests/374086547a3e73d4a68387d29dc56b00/meta/trace.csv -w /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/metatdenovo/.nf-test/tests/374086547a3e73d4a68387d29dc56b00/work

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        Notes:
        • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        nf-core/metatdenovo Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/metatdenovo

        Input/output options

        input
        https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/samplesheet/samplesheet.csv
        outdir
        /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/metatdenovo/.nf-test/tests/374086547a3e73d4a68387d29dc56b00/output

        Assembler options

        assembler
        megahit

        Orf Caller options

        orf_caller
        prodigal

        Functional annotation options

        hmmfiles
        https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/test_data/PF00317.hmm,https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/test_data/PF00848.hmm,https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/test_data/PF03477.hmm,https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/test_data/PF13597.hmm
        skip_eggnog
        true
        skip_kofamscan
        true

        Taxonomy annotation options

        skip_eukulele
        true

        Institutional config options

        config_profile_description
        Minimal test dataset to check pipeline function
        config_profile_name
        Test profile

        Generic options

        pipelines_testdata_base_path
        s3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/
        trace_report_suffix
        2025-02-05_16-07-34

        Core Nextflow options

        configFiles
        /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/metatdenovo/nextflow.config, /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/metatdenovo/nextflow.config, /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/metatdenovo/tests/nextflow.config
        containerEngine
        singularity
        launchDir
        /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/metatdenovo/.nf-test/tests/374086547a3e73d4a68387d29dc56b00
        profile
        test,singularity
        projectDir
        /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/metatdenovo
        runName
        nice_einstein
        userName
        ddl
        workDir
        /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/metatdenovo/.nf-test/tests/374086547a3e73d4a68387d29dc56b00/work

        MultiQC v1.27 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.